Phylogeography of the fungal pathogenHistoplasma capsulatum

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Abstract
Until recently,Histoplasma capsulatumwas believed to harbour three varieties, var.capsulatum(chiefly a New World human pathogen), var.duboisii(an African human pathogen) and var.farciminosum(an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein‐coding genes. At least eight clades were idengified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny.Histoplasma capsulatumvar.capsulatumindividuals were found in all eight clades. The African clade included all of theH. capsulatumvar.duboisiiindividuals as well as individuals of the other two varieties. The 13 individuals of var.farciminosumwere distributed among three phylogenetic species. These findings suggest that the three varieties ofHistoplasmaare phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein‐coding genes with the phylogeny suggests that the radiation ofHistoplasmastarted between 3 and 13 million years ago in Latin America.

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